Index

_

__init__() (ideal_genom.api_client.GeneEnsemblRestClient method) (ideal_genom.api_client.VEPEnsemblRestClient method) (ideal_genom.get_references.AssemblyReferenceFetcher method) (ideal_genom.get_references.Ensembl37Fetcher method) (ideal_genom.get_references.Ensembl38Fetcher method) (ideal_genom.get_references.FetcherLDRegions method) (ideal_genom.get_references.ReferenceDataFetcher method) (ideal_genom.get_references.RefSeqFetcher method) (ideal_genom.gwas.gwas_glm.GWASfixed method) (ideal_genom.gwas.gwas_glmm.GWASrandom method) (ideal_genom.preprocessing.PostImputation.AnnotateVCF method) (ideal_genom.preprocessing.PostImputation.FilterVariants method) (ideal_genom.preprocessing.PostImputation.GetPLINK method) (ideal_genom.preprocessing.PostImputation.IndexVCF method) (ideal_genom.preprocessing.PostImputation.NormalizeVCF method) (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner method) (ideal_genom.preprocessing.PostImputation.ProcessVCF method) (ideal_genom.preprocessing.PostImputation.ReferenceNormalizeVCF method) (ideal_genom.preprocessing.PostImputation.UnzipVCF method) (ideal_genom.preprocessing.preparatory.Preparatory method)

_download_file() (ideal_genom.get_references.AssemblyReferenceFetcher method) (ideal_genom.get_references.ReferenceDataFetcher method) _file_collector() (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner method) _rate_limit() (ideal_genom.api_client.GeneEnsemblRestClient method) (ideal_genom.api_client.VEPEnsemblRestClient method) _run_task() (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner method) _switch_server() (ideal_genom.api_client.VEPEnsemblRestClient method)

A

annotate_snp() (in module ideal_genom.annotations) annotate_top_hits() (ideal_genom.gwas.gwas_glm.GWASfixed method) (ideal_genom.gwas.gwas_glmm.GWASrandom method) annotate_variants() (in module ideal_genom.annotations) annotate_vcf() (ideal_genom.preprocessing.PostImputation.AnnotateVCF method)

annotate_with_ensembl() (in module ideal_genom.annotations) annotate_with_refseq() (in module ideal_genom.annotations) AnnotateVCF (class in ideal_genom.preprocessing.PostImputation) arg_parser() (in module ideal_genom.Helpers) AssemblyReferenceFetcher (class in ideal_genom.get_references)

B

base_url (ideal_genom.get_references.Ensembl37Fetcher attribute) (ideal_genom.get_references.Ensembl38Fetcher attribute) (ideal_genom.get_references.ReferenceDataFetcher attribute) (ideal_genom.get_references.RefSeqFetcher attribute) build (ideal_genom.get_references.Ensembl37Fetcher attribute) (ideal_genom.get_references.Ensembl38Fetcher attribute) (ideal_genom.get_references.ReferenceDataFetcher attribute) (ideal_genom.get_references.RefSeqFetcher attribute) (ideal_genom.preprocessing.PostImputation.ReferenceNormalizeVCF attribute) (ideal_genom.preprocessing.preparatory.Preparatory attribute)

built (ideal_genom.get_references.FetcherLDRegions attribute)

C

calculate_power_binary() (in module ideal_genom.power_comp) calculate_power_quantitative() (in module ideal_genom.power_comp)

compute_grm() (ideal_genom.gwas.gwas_glmm.GWASrandom method) compute_relative_pos() (in module ideal_genom.visualization.manhattan_type) convert_vcf_to_plink() (ideal_genom.preprocessing.PostImputation.GetPLINK method)

D

delete_temp_files() (in module ideal_genom.Helpers) destination (ideal_genom.get_references.FetcherLDRegions attribute) destination_folder (ideal_genom.get_references.Ensembl38Fetcher attribute) (ideal_genom.get_references.ReferenceDataFetcher attribute)

download_file() (in module ideal_genom.Helpers) download_latest() (ideal_genom.get_references.ReferenceDataFetcher method) download_reference_file() (ideal_genom.get_references.AssemblyReferenceFetcher method) draw_zoomed_heatmap() (in module ideal_genom.visualization.zoom_heatmap)

E

Ensembl37Fetcher (class in ideal_genom.get_references) Ensembl38Fetcher (class in ideal_genom.get_references) ENSEMBL_API_URLS (ideal_genom.api_client.VEPEnsemblRestClient attribute) execute_annotate() (ideal_genom.preprocessing.PostImputation.ProcessVCF method) execute_concatenate() (ideal_genom.preprocessing.PostImputation.ProcessVCF method) execute_filter() (ideal_genom.preprocessing.PostImputation.ProcessVCF method) execute_index() (ideal_genom.preprocessing.PostImputation.ProcessVCF method) execute_ld_prunning() (ideal_genom.preprocessing.preparatory.Preparatory method) execute_normalize() (ideal_genom.preprocessing.PostImputation.ProcessVCF method) execute_pc_decomposition() (ideal_genom.preprocessing.preparatory.Preparatory method)

execute_reference_normalize() (ideal_genom.preprocessing.PostImputation.ProcessVCF method) execute_task() (ideal_genom.preprocessing.PostImputation.AnnotateVCF method) (ideal_genom.preprocessing.PostImputation.FilterVariants method) (ideal_genom.preprocessing.PostImputation.IndexVCF method) (ideal_genom.preprocessing.PostImputation.NormalizeVCF method) (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner method) (ideal_genom.preprocessing.PostImputation.ReferenceNormalizeVCF method) (ideal_genom.preprocessing.PostImputation.UnzipVCF method) execute_unzip() (ideal_genom.preprocessing.PostImputation.ProcessVCF method) extract_gz_file() (in module ideal_genom.Helpers)

F

FetcherLDRegions (class in ideal_genom.get_references) file_path (ideal_genom.get_references.AssemblyReferenceFetcher attribute) files (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner attribute) filter_sumstats() (in module ideal_genom.visualization.zoom_heatmap)

filter_variants() (ideal_genom.preprocessing.PostImputation.FilterVariants method) FilterVariants (class in ideal_genom.preprocessing.PostImputation) find_chromosomes_center() (in module ideal_genom.visualization.manhattan_type) fixed_model_association_analysis() (ideal_genom.gwas.gwas_glm.GWASfixed method)

G

GeneEnsemblRestClient (class in ideal_genom.api_client) get_all_genes() (ideal_genom.get_references.ReferenceDataFetcher method) get_beta_binary() (in module ideal_genom.power_comp) get_beta_quantitative() (in module ideal_genom.power_comp) get_bmi_japanese_gwas_sex_dependent() (in module ideal_genom.get_examples) get_chr_to_NC() (in module ideal_genom.annotations) get_closest_gene() (in module ideal_genom.annotations) get_destination_folder() (ideal_genom.get_references.AssemblyReferenceFetcher method) (ideal_genom.get_references.ReferenceDataFetcher method) get_gene_information() (in module ideal_genom.visualization.zoom_heatmap) get_gene_location() (ideal_genom.api_client.GeneEnsemblRestClient method) get_height_japanese_gwas() (in module ideal_genom.get_examples) get_latest_release() (ideal_genom.get_references.Ensembl37Fetcher method) (ideal_genom.get_references.Ensembl38Fetcher method) (ideal_genom.get_references.ReferenceDataFetcher method) (ideal_genom.get_references.RefSeqFetcher method)

get_ld_matrix() (in module ideal_genom.visualization.zoom_heatmap) get_ld_regions() (ideal_genom.get_references.FetcherLDRegions method) get_number_to_chr() (in module ideal_genom.annotations) get_reference_url() (ideal_genom.get_references.AssemblyReferenceFetcher method) get_top_cond_trumpet_quantitative() (in module ideal_genom.get_examples) get_top_hits() (ideal_genom.gwas.gwas_glm.GWASfixed method) (ideal_genom.gwas.gwas_glmm.GWASrandom method) get_top_loci_trumpet_quantitative() (in module ideal_genom.get_examples) get_trumpet_binary_example() (in module ideal_genom.get_examples) get_trumpet_quantitative_example() (in module ideal_genom.get_examples) get_zoomed_data() (in module ideal_genom.visualization.zoom_heatmap) GetPLINK (class in ideal_genom.preprocessing.PostImputation) gtf_file (ideal_genom.get_references.ReferenceDataFetcher attribute) gtf_to_all_genes() (in module ideal_genom.annotations) GWASfixed (class in ideal_genom.gwas.gwas_glm) GWASrandom (class in ideal_genom.gwas.gwas_glmm) gz_file (ideal_genom.get_references.ReferenceDataFetcher attribute)

H

high_ld_file (ideal_genom.preprocessing.preparatory.Preparatory attribute)

I

ideal_genom.annotations module ideal_genom.api_client module ideal_genom.get_examples module ideal_genom.get_references module ideal_genom.gwas.gwas_glm module ideal_genom.gwas.gwas_glmm module ideal_genom.Helpers module ideal_genom.power_comp module ideal_genom.preprocessing.PostImputation module

ideal_genom.preprocessing.preparatory module ideal_genom.visualization.manhattan_type module ideal_genom.visualization.zoom_heatmap module index_vcf() (ideal_genom.preprocessing.PostImputation.IndexVCF method) IndexVCF (class in ideal_genom.preprocessing.PostImputation) input_name (ideal_genom.gwas.gwas_glm.GWASfixed attribute) (ideal_genom.preprocessing.PostImputation.GetPLINK attribute) (ideal_genom.preprocessing.preparatory.Preparatory attribute) input_path (ideal_genom.gwas.gwas_glm.GWASfixed attribute) (ideal_genom.preprocessing.PostImputation.GetPLINK attribute) (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner attribute) (ideal_genom.preprocessing.PostImputation.ProcessVCF attribute) (ideal_genom.preprocessing.preparatory.Preparatory attribute)

L

latest_url (ideal_genom.get_references.Ensembl37Fetcher attribute) (ideal_genom.get_references.Ensembl38Fetcher attribute) (ideal_genom.get_references.ReferenceDataFetcher attribute) (ideal_genom.get_references.RefSeqFetcher attribute)

ld_regions (ideal_genom.get_references.FetcherLDRegions attribute)

M

manhattan_draw() (in module ideal_genom.visualization.manhattan_type) manhattan_process_data() (in module ideal_genom.visualization.manhattan_type) manhattan_type_annotate() (in module ideal_genom.visualization.manhattan_type) max_workers (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner attribute) miami_draw() (in module ideal_genom.visualization.manhattan_type) miami_draw_anno_lines() (in module ideal_genom.visualization.manhattan_type) miami_process_data() (in module ideal_genom.visualization.manhattan_type) module ideal_genom.annotations ideal_genom.api_client ideal_genom.get_examples ideal_genom.get_references ideal_genom.gwas.gwas_glm ideal_genom.gwas.gwas_glmm ideal_genom.Helpers ideal_genom.power_comp ideal_genom.preprocessing.PostImputation ideal_genom.preprocessing.preparatory ideal_genom.visualization.manhattan_type ideal_genom.visualization.zoom_heatmap

N

normalize_vcf() (ideal_genom.preprocessing.PostImputation.NormalizeVCF method)

normalize_with_reference() (ideal_genom.preprocessing.PostImputation.ReferenceNormalizeVCF method) NormalizeVCF (class in ideal_genom.preprocessing.PostImputation)

O

output_name (ideal_genom.gwas.gwas_glm.GWASfixed attribute) (ideal_genom.preprocessing.PostImputation.GetPLINK attribute) (ideal_genom.preprocessing.preparatory.Preparatory attribute) output_path (ideal_genom.gwas.gwas_glm.GWASfixed attribute) (ideal_genom.preprocessing.PostImputation.GetPLINK attribute) (ideal_genom.preprocessing.PostImputation.ParallelTaskRunner attribute) (ideal_genom.preprocessing.PostImputation.ProcessVCF attribute) (ideal_genom.preprocessing.preparatory.Preparatory attribute)

output_prefix (ideal_genom.preprocessing.PostImputation.AnnotateVCF attribute) (ideal_genom.preprocessing.PostImputation.FilterVariants attribute) (ideal_genom.preprocessing.PostImputation.ReferenceNormalizeVCF attribute)

P

ParallelTaskRunner (class in ideal_genom.preprocessing.PostImputation) pattern (ideal_genom.preprocessing.PostImputation.IndexVCF attribute) perform_rest_action() (ideal_genom.api_client.GeneEnsemblRestClient method) (ideal_genom.api_client.VEPEnsemblRestClient method) post_vep_request() (ideal_genom.api_client.VEPEnsemblRestClient method)

Preparatory (class in ideal_genom.preprocessing.preparatory) prepare_aux_files() (ideal_genom.gwas.gwas_glmm.GWASrandom method) prepare_genome() (in module ideal_genom.annotations) prepare_gtf_path() (in module ideal_genom.annotations) ProcessVCF (class in ideal_genom.preprocessing.PostImputation)

R

r2_threshold (ideal_genom.preprocessing.PostImputation.FilterVariants attribute) recompute (ideal_genom.gwas.gwas_glm.GWASfixed attribute) ref_annotation (ideal_genom.preprocessing.PostImputation.AnnotateVCF attribute) reference_file (ideal_genom.get_references.AssemblyReferenceFetcher attribute) (ideal_genom.preprocessing.PostImputation.ReferenceNormalizeVCF attribute)

reference_url (ideal_genom.get_references.AssemblyReferenceFetcher attribute) ReferenceDataFetcher (class in ideal_genom.get_references) ReferenceNormalizeVCF (class in ideal_genom.preprocessing.PostImputation) RefSeqFetcher (class in ideal_genom.get_references) results_dir (ideal_genom.gwas.gwas_glm.GWASfixed attribute) run_gwas_glmm() (ideal_genom.gwas.gwas_glmm.GWASrandom method)

S

shell_do() (in module ideal_genom.Helpers) snp_annotations() (in module ideal_genom.visualization.zoom_heatmap) source (ideal_genom.get_references.Ensembl37Fetcher attribute) (ideal_genom.get_references.Ensembl38Fetcher attribute) (ideal_genom.get_references.ReferenceDataFetcher attribute) (ideal_genom.get_references.RefSeqFetcher attribute)

U

unzip_file_flat() (in module ideal_genom.Helpers) unzip_files() (ideal_genom.preprocessing.PostImputation.UnzipVCF method) unzip_latest() (ideal_genom.get_references.ReferenceDataFetcher method)

unzip_reference_file() (ideal_genom.get_references.AssemblyReferenceFetcher method) UnzipVCF (class in ideal_genom.preprocessing.PostImputation) update_fam() (ideal_genom.preprocessing.PostImputation.GetPLINK method)

V

VEPEnsemblRestClient (class in ideal_genom.api_client)